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{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "Detrprok_wf", 
    "steps": {
        "0": {
            "annotation": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", 
                    "name": "genome annotations"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 231.00001525878906
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"genome annotations\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).", 
                    "name": "read alignments on genome"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 205, 
                "top": 403.00001525878906
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"read alignments on genome\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "Select here the GFF file features that will be considered as initial annotations. Any term added here will cause pre-existing features with this term not to be predicted again by the workflow. Please use a comma separated list and use \"CDS\" rather than \"gene\" for protein coding genes. Suggested value: rRNA,tRNA,ncRNA,CDS", 
            "id": 2, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool clean transcript file", 
                    "name": "optionType"
                }
            ], 
            "name": "clean transcript file", 
            "outputs": [
                {
                    "name": "outputFile", 
                    "type": "gtf"
                }
            ], 
            "position": {
                "left": 457, 
                "top": 218.00001525878906
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFile": {
                    "action_arguments": {
                        "newname": "annotation selection"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFile"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CleanTranscriptFile/1.0.0", 
            "tool_state": "{\"optionType\": \"{\\\"type\\\": \\\"Yes\\\", \\\"value\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 0, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "Technical step (format change).", 
            "id": 3, 
            "input_connections": {
                "input1": {
                    "id": 1, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "BAM-to-SAM", 
            "outputs": [
                {
                    "name": "output1", 
                    "type": "sam"
                }
            ], 
            "position": {
                "left": 428, 
                "top": 400.00001525878906
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutput1": {
                    "action_arguments": {
                        "newname": "Read alignments (SAM format)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "output1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "bam_to_sam", 
            "tool_state": "{\"header\": \"\\\"True\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", 
            "tool_version": "1.0.3", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "Clusters annotated proximal genes into operons. Parameter to be set: op_gap. Genes separated by a gap smaller than op_gap are clustered (suggested value: 10 to 150).", 
            "id": 4, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 2, 
                    "output_name": "outputFile"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool clusterize", 
                    "name": "distance"
                }
            ], 
            "name": "clusterize", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 700, 
                "top": 200.00001525878906
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Annotation with operon-like features"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 1, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {
            "annotation": "Clusters overlapping or proximal reads to produce read clusters. Parameter to be set: clust_gap. Reads separated by a gap smaller than clust_gap are clustered (suggested value: 0 to 20 ; a value of 0 will cluster only overlapping reads while a value of 20 will cluster reads even if they are 20-nt apart)", 
            "id": 5, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 3, 
                    "output_name": "output1"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool clusterize", 
                    "name": "distance"
                }
            ], 
            "name": "clusterize", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 662, 
                "top": 505.00001525878906
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Read clusters (with exon)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", 
            "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 4, \\\"FormatInputFileName\\\": \\\"sam\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "6": {
            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.", 
            "id": 6, 
            "input_connections": {
                "inputFile": {
                    "id": 4, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "remove exon lines", 
            "outputs": [
                {
                    "name": "outputFile", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 892, 
                "top": 221.00001525878906
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFile": {
                    "action_arguments": {
                        "newname": "Annotation with operon-like (without exon)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFile"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "7": {
            "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.", 
            "id": 7, 
            "input_connections": {
                "inputFile": {
                    "id": 5, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "remove exon lines", 
            "outputs": [
                {
                    "name": "outputFile", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 892, 
                "top": 505.00001525878906
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFile": {
                    "action_arguments": {
                        "newname": "Read clusters"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFile"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "8": {
            "annotation": "Technical step: orders the features by increasing positions.", 
            "id": 8, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 6, 
                    "output_name": "outputFile"
                }
            }, 
            "inputs": [], 
            "name": "collapse reads", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1072, 
                "top": 261.00001525878906
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Annotation list with operon-like feature"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/collapseReads/1.0.0", 
            "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"strand\": \"\\\"False\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "9": {
            "annotation": "Selects read clusters that form new independent annotations. Parameter to be set: RNA_gap. Read clusters at a distance from existing annotations larger than RNA_gap are selected (suggested value: 25).", 
            "id": 9, 
            "input_connections": {
                "formatType2|inputFileName2": {
                    "id": 8, 
                    "output_name": "outputFileGff"
                }, 
                "formatType|inputFileName1": {
                    "id": 7, 
                    "output_name": "outputFile"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool compare overlapping small query", 
                    "name": "OptionDistance"
                }
            ], 
            "name": "compare overlapping small query", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1197, 
                "top": 521.0000152587891
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Read clusters not overlapping annotation"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "10": {
            "annotation": "Selects read clusters that overlap annotations in the same direction. Parameter to be set: RNA_gap. A read cluster separated from an annotation by a gap smaller than RNA_gap is selected. Caution: use same RNA_gap value as in previous step!", 
            "id": 10, 
            "input_connections": {
                "formatType2|inputFileName2": {
                    "id": 8, 
                    "output_name": "outputFileGff"
                }, 
                "formatType|inputFileName1": {
                    "id": 7, 
                    "output_name": "outputFile"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool compare overlapping small query", 
                    "name": "OptionDistance"
                }
            ], 
            "name": "compare overlapping small query", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1407, 
                "top": 328.00001525878906
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "Read clusters overlapping annotation"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "11": {
            "annotation": "Selection of read clusters that are antisense of an extended annotation. This step produces a first list of antisense candidates.", 
            "id": 11, 
            "input_connections": {
                "formatType2|inputFileName2": {
                    "id": 8, 
                    "output_name": "outputFileGff"
                }, 
                "formatType|inputFileName1": {
                    "id": 9, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "compare overlapping small query", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1660, 
                "top": 531.0000152587891
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "first list of asRNA"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"100\\\"}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "12": {
            "annotation": "Selection of read clusters that are outside and not in antisense of an extended annotation. This step produces a first list of small RNAs.", 
            "id": 12, 
            "input_connections": {
                "formatType2|inputFileName2": {
                    "id": 8, 
                    "output_name": "outputFileGff"
                }, 
                "formatType|inputFileName1": {
                    "id": 9, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "compare overlapping small query", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1665, 
                "top": 673
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "first list of sRNA"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", 
            "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"100\\\"}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "13": {
            "annotation": "Technical step: merging of annotations and their overlapping read clusters. This will be used to extend annotation.", 
            "id": 13, 
            "input_connections": {
                "input1": {
                    "id": 8, 
                    "output_name": "outputFileGff"
                }, 
                "queries_0|input2": {
                    "id": 10, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [], 
            "name": "Concatenate datasets", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1725, 
                "top": 228.00001525878906
            }, 
            "post_job_actions": {
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "Annotations and read clusters overlapping them"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "cat1", 
            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "14": {
            "annotation": "Filters antisense RNAs based on their size. Parameter to be set: as_min_size. as_min_size is the minimal size for calling an antisense RNA (suggestion: 50).", 
            "id": 14, 
            "input_connections": {
                "formatType|inputFileName": {
                    "id": 11, 
                    "output_name": "outputFileGff"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool restrict from size", 
                    "name": "OptionMin"
                }
            ], 
            "name": "restrict from size", 
            "outputs": [
                {
                    "name": "outputFileGff", 
                    "type": "gff3"
                }
            ], 
            "position": {
                "left": 1959.2166748046875, 
                "top": 548.4833526611328
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutputFileGff": {
                    "action_arguments": {
                        "newname": "asRNA list modified (filtered on their size)"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outputFileGff"
                }
            }, 
            "tool_errors": null, 
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